problem, installing from scratch on our HPC fails while trying to install a perl packages:
Encountered problems while solving:
- package perl-encode-locale-1.05-pl526_6 requires perl >=5.26.2,<5.26.3.0a0, but none of the providers can be installed
I have perl 5.26.3 as default on the system or 5.30.2 or 5.34.1 loadable as module.
thanks for any advice in advance
Version info
- bcbio version (
bcbio_nextgen.py --version): 1.2.9
- OS name and version (
lsb_release -ds):Red Hat Enterprise Linux 8.4
To Reproduce
Exact bcbio command you have used:
/usr/local/bin/python3
../bcbio_nextgen_install.py \
-u stable \
--datatarget variation \
--datatarget rnaseq \
--cores 32 \
--tooldir ${TOOLDIR} \
--isolate \
--distribution "centos" \
--mamba \
--genomes ${GENOMES} \
${DATADIR}
Your yaml configuration file:
Log files (could be found in work/log)
Please attach (10MB max): bcbio-nextgen-commands.log, and bcbio-nextgen-debug.log.
Checking required dependencies
Installing isolated base python installation
Installing mamba
Collecting package metadata (current_repodata.json): done
Solving environment: done
# All requested packages already installed.
Retrieving notices: ...working... done
Installing conda-build
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (0.24.0) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['conda-build', 'mamba=0.24.0']
r/noarch No change
r/linux-64 No change
pkgs/r/linux-64 No change
pkgs/r/noarch No change
ursky/linux-64 No change
ursky/noarch No change
pkgs/main/noarch 817.9kB @ 901.1kB/s 0.3s
bioconda/linux-64 4.5MB @ 4.1MB/s 1.2s
pkgs/main/linux-64 5.0MB @ 3.9MB/s 1.3s
conda-forge/noarch 10.3MB @ 4.4MB/s 2.5s
bioconda/noarch 4.1MB @ 1.6MB/s 1.7s
conda-forge/linux-64 27.8MB @ 4.0MB/s 7.3s
Pinned packages:
- python 3.7.*
Transaction
Prefix: /projects/0/lwc2020006/software/bcbio/1.2.9/data/anaconda
All requested packages already installed
Installing bcbio-nextgen
--2022-11-21 14:05:48-- https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/requirements-conda.txt
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.111.133, 185.199.109.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 20 [text/plain]
Saving to: ‘requirements-conda.txt’
requirements-conda.txt 100%[============================================>] 20 --.-KB/s in 0s
2022-11-21 14:05:48 (2.23 MB/s) - ‘requirements-conda.txt’ saved [20/20]
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (0.24.0) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['bcbio-nextgen']
r/linux-64 Using cache
r/noarch Using cache
conda-forge/linux-64 Using cache
conda-forge/noarch Using cache
bioconda/linux-64 Using cache
bioconda/noarch Using cache
pkgs/main/linux-64 Using cache
pkgs/main/noarch Using cache
pkgs/r/linux-64 Using cache
pkgs/r/noarch Using cache
ursky/noarch No change
ursky/linux-64 No change
Pinned packages:
- python 3.7.*
Transaction
Prefix: /projects/0/lwc2020006/software/bcbio/1.2.9/data/anaconda
All requested packages already installed
Collecting package metadata (current_repodata.json): done
Solving environment: done
# All requested packages already installed.
Retrieving notices: ...working... done
Installing data and third party dependencies
Upgrading bcbio
--2022-11-21 14:06:42-- https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/requirements-conda.txt
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.108.133, 185.199.111.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 20 [text/plain]
Saving to: ‘bcbio-update-requirements.txt’
bcbio-update-requirements.tx 100%[============================================>] 20 --.-KB/s in 0s
2022-11-21 14:06:43 (424 KB/s) - ‘bcbio-update-requirements.txt’ saved [20/20]
Upgrade of bcbio-nextgen code complete.
Upgrading third party tools to latest versions
--2022-11-21 14:06:50-- https://github.com/chapmanb/cloudbiolinux/archive/master.tar.gz
Resolving github.com (github.com)... 140.82.121.4
Connecting to github.com (github.com)|140.82.121.4|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://codeload.github.com/chapmanb/cloudbiolinux/tar.gz/refs/heads/master [following]
--2022-11-21 14:06:51-- https://codeload.github.com/chapmanb/cloudbiolinux/tar.gz/refs/heads/master
Resolving codeload.github.com (codeload.github.com)... 140.82.121.9
Connecting to codeload.github.com (codeload.github.com)|140.82.121.9|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/x-gzip]
Saving to: ‘STDOUT’
0K ........ ........ ........ ........ ........ ........ 6.55M
3072K ........ ........ ........ ....... 32.6M=0.5s
2022-11-21 14:06:51 (9.56 MB/s) - written to stdout [5195149]
Reading packages from /gpfs/work2/0/lwc2020006/software/bcbio/1.2.9/tmpbcbio-install/cloudbiolinux/contrib/flavor/ngs_pipeline_minimal/packages-conda.yaml
Checking for problematic or migrated packages in default environment
Initalling initial set of packages for default environment with mamba
# Installing into conda environment default: age-metasv, atropos, bamtools, bamutil, bbmap, bcftools=1.13, bedops, bio-vcf, biobambam=2.0.87, bowtie, break-point-inspector, bwa, cage, cnvkit, coincbc, cramtools, deeptools, express, fastp, fastqc, geneimpacts, genesplicer, gffcompare, goleft, grabix, gsort, gsutil, gvcfgenotyper, h5py=3.3, hdf5=1.10, hisat2, hmmlearn, htseq, impute2, kallisto=0.46, kraken, ldc, macs2, maxentscan, mbuffer, minimap2, mintmap, mirdeep2, mirtop, moreutils, multiqc, multiqc-bcbio, ngs-disambiguate, novoalign, oncofuse, pandoc, parallel, pbgzip, peddy, pizzly, pythonpy, qsignature, rapmap, rtg-tools, sailfish, salmon, samblaster, samtools=1.13, scalpel, seq2c<2016, seqbuster, seqcluster, seqtk, sickle-trim, simple_sv_annotation, singlecell-barcodes, snap-aligner=1.0dev.97, snpeff=5.0, solvebio, spades, star=2.6.1d, stringtie, subread, survivor, tdrmapper, tophat-recondition, trim-galore, ucsc-bedgraphtobigwig, ucsc-bedtobigbed, ucsc-bigbedinfo, ucsc-bigbedsummary, ucsc-bigbedtobed, ucsc-bigwiginfo, ucsc-bigwigsummary, ucsc-bigwigtobedgraph, ucsc-bigwigtowig, ucsc-fatotwobit, ucsc-gtftogenepred, ucsc-liftover, ucsc-wigtobigwig, umis, vardict-java, vardict<=2015, variantbam, varscan, vcfanno, viennarna, vqsr_cnn, wham, ipyparallel=6.3.0, ipython-cluster-helper=0.6.4=py_0, ipython=7.29.0, ipython_genutils=0.2.0=py37_0, traitlets=4.3.3, anaconda-client, awscli, bzip2, ncurses, nodejs, p7zip, readline, s3gof3r, xz, perl-app-cpanminus, perl-archive-extract, perl-archive-zip, perl-bio-db-sam, perl-cgi, perl-dbi, perl-encode-locale, perl-file-fetch, perl-file-sharedir, perl-file-sharedir-install, perl-ipc-system-simple, perl-lwp-protocol-https, perl-lwp-simple, perl-sanger-cgp-battenberg, perl-statistics-descriptive, perl-time-hires, perl-vcftools-vcf, bioconductor-annotate, bioconductor-apeglm, bioconductor-biocgenerics, bioconductor-biocinstaller, bioconductor-biocstyle, bioconductor-biostrings, bioconductor-biovizbase, bioconductor-bsgenome.hsapiens.ucsc.hg19, bioconductor-bsgenome.hsapiens.ucsc.hg38, bioconductor-bubbletree, bioconductor-cn.mops, bioconductor-copynumber, bioconductor-degreport, bioconductor-deseq2, bioconductor-dexseq, bioconductor-dnacopy, bioconductor-genomeinfodb, bioconductor-genomeinfodbdata, bioconductor-genomeinfodbdata, bioconductor-genomicranges, bioconductor-iranges, bioconductor-limma, bioconductor-org.hs.eg.db, bioconductor-purecn>=2.0.1, bioconductor-rhdf5, bioconductor-rtracklayer, bioconductor-rtracklayer, bioconductor-summarizedexperiment, bioconductor-titancna, bioconductor-txdb.hsapiens.ucsc.hg19.knowngene, bioconductor-txdb.hsapiens.ucsc.hg38.knowngene, bioconductor-tximport, bioconductor-vsn, r-base=4.1.1=hb67fd72_0, r-chbutils, r-deconstructsigs, r-devtools, r-dplyr, r-dt, r-ggdendro, r-ggplot2, r-ggrepel, r-gplots, r-gsalib, r-janitor, r-knitr, r-optparse, r-pheatmap, r-plyr, r-pscbs, r-reshape, r-rmarkdown, r-rsqlite, r-sleuth, r-snow, r-stringi, r-tidyverse, r-viridis, r-wasabi, r=4.1=r41hd8ed1ab_1004, xorg-libxt
Encountered problems while solving:
- package perl-encode-locale-1.05-pl526_6 requires perl >=5.26.2,<5.26.3.0a0, but none of the providers can be installed
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... cdfailed with initial frozen solve. Retrying with flexible solve.
Solving environment: ...working... ^[[A^[[A^[[A
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
Your yaml configuration file:
**Log files (could be found in work/log)**
Please attach (10MB max): `bcbio-nextgen-commands.log`, and `bcbio-nextgen-debug.log`.
![[main_samview] fail to read the header from](https://avatars.githubusercontent.com/u/118458917?v=4)
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